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Ask HN: How close are we to replace animal models with software?

news.ycombinator.com

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Re: Ask HN: How close are we to replace animal models with software?

#31

Post by wildermuthn »

pton_xd wrote: post #26
wildermuthn wrote: post #19

Biology is an organic computation that runs at the speed of existence. There may be no way to simulate this computation in silicon at the same scale, insofar as biology is already massively parallel and may very well involve quantum computation. Put another way, if we accept for a moment that the universe is a simulation, it may be fundamentally impossible for an in-simulation simulator to ever reach the computationa…

So what you're saying is, the most efficient AI is not a data center of GPUs, it's... a giant tank of lab-grown brains.

As a counter to my original thought, perhaps simulating the computation of a skull-sized organic system is possible by building an earth-sized silicon system.

Re: Ask HN: How close are we to replace animal models with software?

#32

Post by typon »

amelius wrote: post #14
typon wrote: post #10

Earlier quoted context omitted.

I can imagine a world where you can simulate a simple organism like a worm without knowing how to simulate the cells that make it. This is because emergent behaviour of complex systems can be much simpler than the constituent parts of that system (temperature vs. knowing particle velocities).

How are you going to simulate the administering of a medicinal molecule? Or the knocking out of a gene?

My modelling the relevant parts of the worm that are involved in these processes.

You don't need an atomistic DFT simulator to get a good enough simulation of fluid dynamics, enough to design jets or rockets that go into space.

Re: Ask HN: How close are we to replace animal models with software?

#33

Post by awb »

h1fra wrote: post #12
snek_case wrote: post #4

We can't even simulate a single cell. At least not accurately. You'd need to be able to simulate ribosomes, gene expression, epigenetic factors. Still a lot we don't understand because even single cells are incredibly complex electrochemical machines.

I agree but we also don't know what gravity is, and yet we can compute it with some degree of error. There might be a world we can just approximate enough of this cell, that the details matter less.

This actually illustrates the crux of the problem. Gravity is a single (highly accurate) approximation when applied to 2 objects. But when you have 3 objects interacting with each other, the system is chaotic: https://en.m.wikipedia.org/wiki/Three-body_problem

Even if we could estimate all the molecules, cells, and processes of a biological entity to a similar precision as gravity, the errors would compound exponentially.

Re: Ask HN: How close are we to replace animal models with software?

#34

Post by JPLeRouzic »

yathern wrote: post #21
typon wrote: post #10

Earlier quoted context omitted.

I can imagine a world where you can simulate a simple organism like a worm without knowing how to simulate the cells that make it. This is because emergent behaviour of complex systems can be much simpler than the constituent parts of that system (temperature vs. knowing particle velocities).

I can write a program today that can simulate a worms "emergent behavior" without simulating the cells. Maybe a little 3D model that wriggles around. I can even do a human! But I think what we're looking for here is something closer to emulation. In the same way that video game console emulators seek to reproduce the exact bugs that the original hardware produced - the value here does not come from abstracting away t…

> the value here does not come from abstracting away the lowest levels of behavior

I totally agree.

Re: Ask HN: How close are we to replace animal models with software?

#36

Post by amelius »

typon wrote: post #32
amelius wrote: post #14

Earlier quoted context omitted.

How are you going to simulate the administering of a medicinal molecule? Or the knocking out of a gene?

My modelling the relevant parts of the worm that are involved in these processes. You don't need an atomistic DFT simulator to get a good enough simulation of fluid dynamics, enough to design jets or rockets that go into space.

> modelling the relevant parts of the worm that are involved in these processes.

You mean cell chemistry?

Re: Ask HN: How close are we to replace animal models with software?

#38

Post by JPLeRouzic »

Metacelsus wrote: post #3

Biologist here. We're definitely not close to replacing animal models with software. However, many aspects of animal models can be studied using cell culture systems. I work on ovarian organoids, which can be used to develop fertility therapies. Still, organoids will merely reduce the number of animals used in drug development rather than eliminating them entirely. Before giving a drug to humans, testing whether it's…

> Something that can model heart rate and blood pressure won't be able to say if a cancer drug will work (or if it will have a toxic side effect)

Thanks for having a look at Biogears.

(edit) Please have a look at: "Constraint-based modelling predicts metabolic signatures of low and high-grade serous ovarian cancer"

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344801/

https://github.com/katemeeson/repository_to_accompany_paper_...

Most successful pre-clinical trials *fail* at predicting phase III success. The ratio is enormous. It's time to put some effort into alternative approaches.

Re: Ask HN: How close are we to replace animal models with software?

#40

Post by ewjt »

the_real_cher wrote: post #6

Biology is a borderline infinite system depending on how deep you go. We need to be able to model molecular forcefields to be able to model DNA expression to be able to model protein expression to be able to model, layers and layers of higher order molecules just to represent a cell. Then...you have combining cells to make an organism and the interaction of the organism with its environment which affects all of the a…

Do you actually need to simulate at that minuscule level of detail?

Or is it possible for a system to be built that can approximate biology similar to how LLMs approximate cognition without true understanding and reasoning?

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